Pyne et al. (2009) present three datasets in their manuscript. Analysis results for the T cell phosphorylation data are available on the GenePattern ftp site. To view the clusters identified by FLAME for a given sample in this published data, use the FLAMEContourViewer.Pipeline. The pipeline first runs the FLAMEContourDataGenerator module to generate the data required to display a 3-D contour plot of the clusters in a given sample. It then opens the FLAMEViewer to display a 3-D scatterplot and 3-D contour plot of the clusters in the sample.
To launch FLAMEViewer from GenePattern, you need to first install Java 3D as outlined in this FAQ.
Result: GenePattern displays its main page.
Result: GenePattern displays the FLAMEContourViewer.Pipeline page. It automatically populates the parameter fields with the result files for the selected sample.
Pyne et al. (2009) clustered four channels: SLP76,ZAP70,CD4,CD45RA. The FLAMEViewer uses three channels to display a 3-D contour plot of the clusters in the sample. Select the three channels to use (default: SLP76,ZAP70,CD4).
Result: GenePattern runs the FLAMEContourDataGenerator to generate data for the 3-D contour plot. It then opens the FLAMEViewer to display both a 3-D scatterplot and 3-D contour plot of the clusters in the sample. For instructions on how to use the viewer, see the FLAMEViewer documentation .
The following table lists the samples in the T cell phosphorylation dataset analyzed in Pyne et al. (2009). The parameters used for the analysis are available at ftp://ftp.broadinstitute.org/pub/genepattern/example_files/FLAME/phospho.lymphgated.pipeline.parameters.txt. Use the previous procedure to display analysis results for a selected sample.